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Veloso TGR, da Silva MDCS, Moreira TR, da Luz JMR, Moreli AP, Kasuya MCM, Pereira LL. Microbiomes associated with Coffea arabica and Coffea canephora in four different floristic domains of Brazil. Sci Rep 2023; 13:18477. [PMID: 37898712 PMCID: PMC10613301 DOI: 10.1038/s41598-023-45465-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 10/19/2023] [Indexed: 10/30/2023] Open
Abstract
Brazilian coffee production relies on the cultivation of Coffea arabica and Coffea canephora. Climate change has been responsible for the decreasing yield of the crops in the country yet the associated microbial community can mitigate these effects by improving plant growth and defense. Although some studies have tried to describe the microorganisms associated with these Coffea species, a study that compares the microbiome on a wider spatial scale is needed for a better understanding of the terroir of each coffee planting region. Therefore, our aim was to evaluate the microbial communities harbored in soils and fruits of these Coffea species in four Brazilian floristic domains (Amazon, Atlantic Forest Caatinga, and Cerrado). One hundred and eight samples (90 of soil and 90 of fruits) were used in the extraction and sequencing of the fungal and bacterial DNA. We detected more than 1000 and 500 bacterial and fungal genera, respectively. Some soil microbial taxa were more closely related to one coffee species than the other species. Bacillus bataviensis tends to occur more in arid soils from the Caatinga, while the fungus Saitozyma sp. was more related to soils cultivated with C. arabica. Thus, the species and the planting region (floristic domain) of coffee affect the microbial composition associated with this crop. This study is the first to report microbial communities associated with coffee produced in four floristic domains that include sites in eight Brazilian states. Data generated by DNA sequencing provides new insights into microbial roles and their potential for the developing more sustainable coffee management, such as the production of biofertilizers and starter culture for fermentation of coffee cherries.
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Affiliation(s)
- Tomás Gomes Reis Veloso
- Departamento de Microbiologia, Universidade Federal de Viçosa, Laboratory of Mycorrhizal Associations - LAMIC, Avenida PH Rolfs S/N, Viçosa, CEP, Minas Gerais, 36570-000, Brazil
| | - Marliane de Cássia Soares da Silva
- Departamento de Microbiologia, Universidade Federal de Viçosa, Laboratory of Mycorrhizal Associations - LAMIC, Avenida PH Rolfs S/N, Viçosa, CEP, Minas Gerais, 36570-000, Brazil
| | - Taís Rizzo Moreira
- Universidade Federal do Espírito Santo. Centro de Ciências Agrárias e Engenharias. Av. Gov. Lindemberg, 316 - Centro, Jerônimo Monteiro, CEP, Espírito Santo, 29550-000, Brazil
| | - José Maria Rodrigues da Luz
- Departamento de Microbiologia, Universidade Federal de Viçosa, Laboratory of Mycorrhizal Associations - LAMIC, Avenida PH Rolfs S/N, Viçosa, CEP, Minas Gerais, 36570-000, Brazil
| | - Aldemar Polonini Moreli
- Instituto Federal do Espírito Santo. Coffee Design. Avenida Elizabeth Minete Perim, S/N, Bairro São Rafael, Venda Nova do Imigrante, CEP, Espírito Santo, 29375-000, Brazil
| | - Maria Catarina Megumi Kasuya
- Departamento de Microbiologia, Universidade Federal de Viçosa, Laboratory of Mycorrhizal Associations - LAMIC, Avenida PH Rolfs S/N, Viçosa, CEP, Minas Gerais, 36570-000, Brazil
| | - Lucas Louzada Pereira
- Instituto Federal do Espírito Santo. Coffee Design. Avenida Elizabeth Minete Perim, S/N, Bairro São Rafael, Venda Nova do Imigrante, CEP, Espírito Santo, 29375-000, Brazil.
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Yoshida K, Ueno T, Koito K, Hu D, Yamaguchi A. A Comparative Study on Fungal Diversity in Organic and Conventionally Cultivated Lemons During Accelerated Storage. Curr Microbiol 2023; 80:69. [PMID: 36609598 DOI: 10.1007/s00284-022-03164-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 12/23/2022] [Indexed: 01/08/2023]
Abstract
There has been a growing interest in organic farming as a countermeasure to the environmental burden caused by chemical pesticides. We analyzed and compared the fungal diversity of lemon fruits from organic and conventional cultivation by automated rRNA intergenic spacer analysis (ARISA), accompanied by isolation of cultured colonies and metagenomic analysis. Lemon peels were cut out and subjected to the analyses at purchase and after accelerated storage at 28 °C. The organic lemons did not decay even after 14 weeks, while most of the conventional lemons did decay. The fungal colony counts were not significantly different, although the number of fungal species together with the Shannon index, considering the abundance of each species, clearly showed more diversity in organic lemons than in conventional lemons (p = 0.011). Fusarium sp. (putative F. solani) accounted for as much as 90% of the relative abundance in the decayed conventional lemons. Metagenomic analysis also supported the lack of fungal diversity in conventional lemons. These results may suggest that organic cultivation maintains the diversity of native fungal flora in lemon fruit and could contribute to preventing decay during ambient storage.
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Affiliation(s)
- Kuniko Yoshida
- Department of Food Science and Human Wellness, Rakuno Gakuen University, Midorimachi 582, Bunkyodai, Ebetsu-Shi, Hokkaido, 069-8501, Japan
| | - Takeshi Ueno
- Department of Food Science and Human Wellness, Rakuno Gakuen University, Midorimachi 582, Bunkyodai, Ebetsu-Shi, Hokkaido, 069-8501, Japan
| | - Kentaro Koito
- Department of Sustainable Agriculture, Rakuno Gakuen University, Midorimachi 582, Bunkyodai, Ebetsu-Shi, Hokkaido, 069-8501, Japan
| | - Dagula Hu
- Department of Food Science and Human Wellness, Rakuno Gakuen University, Midorimachi 582, Bunkyodai, Ebetsu-Shi, Hokkaido, 069-8501, Japan
| | - Akihiro Yamaguchi
- Department of Food Science and Human Wellness, Rakuno Gakuen University, Midorimachi 582, Bunkyodai, Ebetsu-Shi, Hokkaido, 069-8501, Japan.
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Kestel JH, Field DL, Bateman PW, White NE, Allentoft ME, Hopkins AJM, Gibberd M, Nevill P. Applications of environmental DNA (eDNA) in agricultural systems: Current uses, limitations and future prospects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 847:157556. [PMID: 35882340 DOI: 10.1016/j.scitotenv.2022.157556] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/29/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
Global food production, food supply chains and food security are increasingly stressed by human population growth and loss of arable land, becoming more vulnerable to anthropogenic and environmental perturbations. Numerous mutualistic and antagonistic species are interconnected with the cultivation of crops and livestock and these can be challenging to identify on the large scales of food production systems. Accurate identifications to capture this diversity and rapid scalable monitoring are necessary to identify emerging threats (i.e. pests and pathogens), inform on ecosystem health (i.e. soil and pollinator diversity), and provide evidence for new management practices (i.e. fertiliser and pesticide applications). Increasingly, environmental DNA (eDNA) is providing rapid and accurate classifications for specific organisms and entire species assemblages in substrates ranging from soil to air. Here, we aim to discuss how eDNA is being used for monitoring of agricultural ecosystems, what current limitations exist, and how these could be managed to expand applications into the future. In a systematic review we identify that eDNA-based monitoring in food production systems accounts for only 4 % of all eDNA studies. We found that the majority of these eDNA studies target soil and plant substrates (60 %), predominantly to identify microbes and insects (60 %) and are biased towards Europe (42 %). While eDNA-based monitoring studies are uncommon in many of the world's food production systems, the trend is most pronounced in emerging economies often where food security is most at risk. We suggest that the biggest limitations to eDNA for agriculture are false negatives resulting from DNA degradation and assay biases, as well as incomplete databases and the interpretation of abundance data. These require in silico, in vitro, and in vivo approaches to carefully design, test and apply eDNA monitoring for reliable and accurate taxonomic identifications. We explore future opportunities for eDNA research which could further develop this useful tool for food production system monitoring in both emerging and developed economies, hopefully improving monitoring, and ultimately food security.
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Affiliation(s)
- Joshua H Kestel
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia; Molecular Ecology and Evolution Group (MEEG), School of Science, Edith Cowan University, Joondalup 6027, Australia.
| | - David L Field
- Molecular Ecology and Evolution Group (MEEG), School of Science, Edith Cowan University, Joondalup 6027, Australia
| | - Philip W Bateman
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia; Behavioural Ecology Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
| | - Nicole E White
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
| | - Morten E Allentoft
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia; Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
| | - Anna J M Hopkins
- Molecular Ecology and Evolution Group (MEEG), School of Science, Edith Cowan University, Joondalup 6027, Australia
| | - Mark Gibberd
- Centre for Crop Disease Management (CCDM), School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
| | - Paul Nevill
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
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Epichloë Increases Root Fungal Endophyte Richness and Alters Root Fungal Endophyte Composition in a Changing World. J Fungi (Basel) 2022; 8:jof8111142. [DOI: 10.3390/jof8111142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/24/2022] [Accepted: 10/27/2022] [Indexed: 11/16/2022] Open
Abstract
Plants harbor a variety of fungal symbionts both above- and belowground, yet little is known about how these fungi interact within hosts, especially in a world where resource availability is changing due to human activities. Systemic vertically transmitted endophytes such as Epichloë spp. may have particularly strong effects on the diversity and composition of later-colonizing symbionts such as root fungal endophytes, especially in primary successional systems. We made use of a long-term field experiment in Great Lakes sand dunes to test whether Epichloë colonization of the dune-building grass, Ammophila breviligulata, could alter fungal root endophyte species richness or community composition in host plants. We also tested whether nitrogen addition intensified the effects of Epichlöe on the root endophyte community. We found that Epichloë increased richness of root endophytes in Ammophila by 17% overall, but only shifted community composition of root endophytes under nitrogen-enriched conditions. These results indicate that Epichlöe acts as a key species within Ammophila, changing richness and composition of the root mycobiome and integrating above- and belowground mycobiome interactions. Further, effects of Epichloë on root endophyte communities were enhanced by N addition, indicating that this fungal species may become even more important in future environments.
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Gagliardi S, Avelino J, Fulthorpe R, Virginio Filho EDM, Isaac ME. No evidence of foliar disease impact on crop root functional strategies and soil microbial communities: what does this mean for organic coffee? OIKOS 2022. [DOI: 10.1111/oik.08987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Jacques Avelino
- CIRAD, UMR PHIM Montpellier France
- PHIM, Univ. Montpellier, CIRAD, INRAE, Inst. Agro, IRD Montpellier France
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Aldrich-Wolfe L, Black KL, Hartmann EDL, Shivega WG, Schmaltz LC, McGlynn RD, Johnson PG, Asheim Keller RJ, Vink SN. Taxonomic shifts in arbuscular mycorrhizal fungal communities with shade and soil nitrogen across conventionally managed and organic coffee agroecosystems. MYCORRHIZA 2020; 30:513-527. [PMID: 32500441 DOI: 10.1007/s00572-020-00967-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 05/20/2020] [Indexed: 06/11/2023]
Abstract
The composition of arbuscular mycorrhizal fungal (AMF) communities should reflect not only responses to host and soil environments, but also differences in functional roles and costs vs. benefits among arbuscular mycorrhizal fungi. The coffee agroecosystem allows exploration of the effects of both light and soil fertility on AMF communities, because of the variation in shade and soil nutrients farmers generate through field management. We used high-throughput ITS2 sequencing to characterize the AMF communities of coffee roots in 25 fields in Costa Rica that ranged from organic management with high shade and no chemical fertilizers to conventionally managed fields with minimal shade and high N fertilization, and examined relationships between AMF communities and soil and shade parameters with partial correlations, NMDS, PERMANOVA, and partial least squares analysis. Gigasporaceae and Acaulosporaceae dominated coffee AMF communities in terms of relative abundance and richness, respectively. Gigasporaceae richness was greatest in conventionally managed fields, while Glomeraceae richness was greatest in organic fields. While total AMF richness and root colonization did not differ between organic and conventionally managed fields, AMF community composition did; these differences were correlated with soil nitrate and shade. OTUs differing in relative abundance between conventionally managed and organic fields segregated into four groups: Gigasporaceae associated with high light and nitrate availability, Acaulosporaceae with high light and low nitrate availability, Acaulosporaceae and a single relative of Rhizophagus fasciculatus with shade and low nitrate availability, and Claroideoglomus/Glomus with conventionally managed fields but uncorrelated with shade and soil variables. The association of closely related taxa with similar shade and light availabilities is consistent with phylogenetic trait conservatism in AM fungi.
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Affiliation(s)
- Laura Aldrich-Wolfe
- Department of Biological Sciences, North Dakota State University, Fargo, ND, USA.
| | - Katie L Black
- Biology Department, Concordia College, Moorhead, MN, USA
| | | | - W Gaya Shivega
- Biology Department, Concordia College, Moorhead, MN, USA
| | | | | | | | | | - Stefanie N Vink
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, the Netherlands
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